Zygotic genome activation (ZGA) is a universal process in early embryogenesis of
metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the …

More than half the human and mouse genomes are comprised of repetitive sequences, such
as transposable elements (TEs), which have been implicated in many biological processes …

Gene-by-environment (GxE) interactions determine common disease risk factors and
biomedically relevant complex traits. However, quantifying how the environment modulates …

Histone modifications are now well-established mediators of transcriptional programs that
distinguish cell states. However, the kinetics of histone modification and their role in …

Efficient predictive biomarkers are needed for immune checkpoint inhibitor (ICI)-based
immunotherapy in non-small cell lung cancer (NSCLC). Testing the predictive value of …

Variations in noncoding regulatory sequences play a central role in evolution. Interpreting
such variations, however, remains difficult even in the context of defined attributes such as …

Noncoding regulatory variants play a central role in the genetics of human diseases and in
evolution. Here we measure allele-specific transcription factor binding occupancy of three …

Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into
transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of …

Functional variants in the genome are usually identified by their association with local gene
expression, DNA methylation or chromatin states. DNA sequence motif analysis and …

Precise patterns of gene expression are driven by interactions between transcription factors,
regulatory DNA sequences, and chromatin. How DNA mutations affecting any one of these …